Blog

Ladha JK, Jat ML, Stirling CM, Chakraborty D, Pradhan P, Krupnik TJ et al. Achieving the sustainable development goals in agriculture: The crucial role of nitrogen in cereal-based systems. In: Sparks DL, editor. Advances in Agronomy, Vol 163. Advances in Agronomy. 1632020. pp. 39–116.

Menegat S, Ledo A, Tirado R. Greenhouse gas emissions from global production and use of nitrogen synthetic fertilisers in agriculture. Sci Rep. 2022;12(1):14490.

Chauhan BSJ, Khawar J, Mahajan G. Rice production worldwide. Springer. 2017;247.

Xu JZ, Peng SZ, Yang SH, Wang WG. Ammonia volatilization losses from a rice paddy with different irrigation and nitrogen managements. Agric Water Manage. 2012;104:184–92.

Article 

Google Scholar 

Hu B, Wang W, Chen JJ, Liu YQ, Chu CC. Genetic improvement toward nitrogen-use efficiency in rice: lessons and perspectives. Mol Plant. 2023;16(1):64–74.

Article 
CAS 
PubMed 

Google Scholar 

Neeraja CN, Barbadikar KM, Mangrauthia SK, Rao PR, Subrahmanayam D, Sundaram RM. Genes for NUE in rice: a way forward for molecular breeding and genome editing. Plant Physiol Rep. 2021;26(4):587–99.

Article 
CAS 

Google Scholar 

Cassman KG, Peng S, Olk DC, Ladha JK, Reichardt W, Dobermann A, et al. Opportunities for increased nitrogen-use efficiency from improved resource management in irrigated rice systems. Field Crops Res. 1998;56(1–2):7–39.

Article 

Google Scholar 

Li H, Hu B, Chu CC. Nitrogen use efficiency in crops: lessons from Arabidopsis and rice. J Exp Bot. 2017;68(10):2477–88.

Article 
CAS 
PubMed 

Google Scholar 

Reig-Valiente J, Viruel J, Sales E, Marqués L, Terol J, Gut M et al. Genetic diversity and population structure of rice varieties cultivated in temperate regions. Rice. 2016;9:58.

Andaya VC, Tai TH. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet. 2006;113(3):467–75.

Article 
CAS 
PubMed 

Google Scholar 

Hour AL, Hsieh WH, Chang SH, Wu YP, Chin HS, Lin YR. Genetic diversity of landraces and improved varieties of rice (Oryza sativa L.) in Taiwan. Rice. 2020;13:82.

Kumar V, Rithesh L, Raghuvanshi N, Kumar A, Parmar K. Advancing nitrogen use efficiency in cereal crops: A comprehensive exploration of genetic manipulation, nitrogen dynamics, and plant nitrogen assimilation. South Afr J Bot. 2024;169:486–98.

Article 
CAS 

Google Scholar 

Nazish T, Arshad M, Jan SU, Javaid A, Khan MH, Naeem MA, et al. Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L). Transgenic Res. 2022;31(1):23–42.

Article 
CAS 
PubMed 

Google Scholar 

Hou MM, Yu M, Li ZQ, Ai ZY, Chen JG. Molecular regulatory networks for improving nitrogen use efficiency in rice. Int J Mol Sci. 2021;22(16):9040.

Chaudhary S, Kalkal M. Rice transcriptome analysis reveals nitrogen starvation modulates differential alternative splicing and transcript usage in various Metabolism-Related genes. Life-Basel. 2021;11(4):285.

Feng Y, Lu Q, Zhai RR, Zhang MC, Xu Q, Yang YL, et al. Genome wide association mapping for grain shape traits in indica rice. Planta. 2016;244(4):819–30.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Qiu XJ, Zhu SB, Hu H, Wang CC, Lv WK, He LP, et al. Genome-Wide association mapping for grain shape in rice accessions. Int J Agric Biology. 2020;23(3):582–8.

CAS 

Google Scholar 

Liu YZ, Xin W, Chen LQ, Liu YQ, Wang X, Ma C et al. Genome-Wide association analysis of effective tillers in rice under different nitrogen gradients. Int J Mol Sci. 2024;25(5):2969.

Cheng XP, Chang YP, Sun JH, Du MY, Liang LP, Zhang MY et al. Identification of candidate genes and favourable haplotypes for yield traits in rice based on a genome-wide association study. Euphytica. 2023;219(12):125.

Peng SS, Liu YC, Xu YC, Zhao JH, Gao P, Liu Q et al. Genome-Wide association study identifies a Plant-Height-Associated Gene OsPG3 in a population of commercial rice varieties. Int J Mol Sci. 2023;24(14):11454.

Rakotoson T, Dusserre J, Letourmy P, Frouin J, Ratsimiala IR, Rakotoarisoa NV, et al. Genome-Wide association study of nitrogen use efficiency and agronomic traits in upland rice. Rice Sci. 2021;28(4):379–90.

Article 

Google Scholar 

Wang YY, Cheng YH, Chen KE, Tsay YF. Nitrate Transport, Signaling, and Use Efficiency. In: Merchant SS, editor. Annual Review of Plant Biology, Vol 69. Annual Review of Plant Biology. 692018. pp. 85–122.

Wei D, Cui KH, Ye GY, Pan JF, Xiang J, Huang JL, et al. QTL mapping for nitrogen-use efficiency and nitrogen-deficiency tolerance traits in rice. Plant Soil. 2012;359(1–2):281–95.

Article 
CAS 

Google Scholar 

Li Q, Lu XL, Wang CJ, Shen L, Dai LP, He JL, et al. Genome-wide association study and transcriptome analysis reveal new QTL and candidate genes for nitrogen-deficiency tolerance in rice. Crop J. 2022;10(4):942–51.

Article 
CAS 

Google Scholar 

Ding CQ, You J, Chen L, Wang SH, Ding YF. Nitrogen fertilizer increases spikelet number per panicle by enhancing cytokinin synthesis in rice. Plant Cell Rep. 2014;33(2):363–71.

Article 
CAS 
PubMed 

Google Scholar 

Das K, Panda BB, Shaw BP, Das SR, Dash SK, Kariali E et al. Grain density and its impact on grain filling characteristic of rice: mechanistic testing of the concept in genetically related cultivars. Sci Rep. 2018;8:4149.

Gao HB, Wang WG, Wang YH, Liang Y. Molecular mechanisms underlying plant architecture and its environmental plasticity in rice. Mol Breeding. 2019;39(12):167.

Dou Z, Zhou YC, Zhang YY, Guo W, Xu Q, Gao H. Influence of nitrogen applications during grain-Filling stage on rice (Oryza sativa L.) yield and grain quality under high temperature. Agronomy-Basel. 2024;14(1):216.

Li RH, Li MJ, Ashraf U, Liu SW, Zhang JE. Exploring the relationships between yield and yield-Related traits for rice varieties released in China from 1978 to 2017. Front Plant Sci. 2019;10:543.

Zhang QG, Sun J, Wang LP, Chen J, Ke J, Wu LQ. Effects of nitrogen application at different panicle development stages on the panicle structure and grain yield in hybrid indica rice cultivars. Agronomy-Basel. 2025;15(3):595.

Xin W, Wang JG, Li J, Zhao HW, Liu HL, Zheng HL et al. Candidate gene analysis for nitrogen absorption and utilization in Japonica rice at the seedling stage based on a Genome-Wide association study. Front Plant Sci. 2021;12:670861.

García-Romeral J, Castanera R, Casacuberta J, Domingo C. Deciphering the genetic basis of allelopathy in japonica rice cultivated in temperate regions using a Genome-Wide association study. Rice. 2024;17(1):22.

Walkley A, Black IA. An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci. 1934;37(1):29–38.

Article 
CAS 

Google Scholar 

Bouyoucos GJ. The hydrometer as a new method for the mechanical analysis of soils. Soil Sci. 1927;23(5):343–54.

Article 
CAS 

Google Scholar 

Lancashire PD, Bleiholder H, Vandenboom T, Langeluddeke P, Stauss R, Weber E, et al. A uniform decimal code for growth-stages of crops and weeds. Ann Appl Biol. 1991;119(3):561–601.

Article 

Google Scholar 

Inc. SI. JMP^®. 16 ed. Cary, NC: SAS Institute Inc.; 1989–2023.

Team RC. R: A Language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2023.

Google Scholar 

Kowarik A, Templ M. Imputation with the R package VIM. J Stat Softw. 2016;74(7):1–16.

Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23(19):2633–5.

Article 
CAS 
PubMed 

Google Scholar 

Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2006;38(2):203–8.

Article 
CAS 
PubMed 

Google Scholar 

Patil I. Visualizations with statistical details: the ‘ggstatsplot’ approach. J Open Source Softw. 2021;6:3167.

Article 

Google Scholar 

Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, et al. Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 2013;54(2):e6.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Volume 6. New York, NY: Rice; 2013. p. 4. 1.

Google Scholar 

McCouch SR, Rice Genetics C. Gene nomenclature system for rice. Rice. 2008;1(1):72–84.

Article 

Google Scholar 

Kurata N, Yamazaki Y, Oryzabase. An integrated biological and genome information database for rice. Plant Physiol. 2006;140(1):12–7.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, et al. Rice SNP-seek database update: new snps, indels, and queries. Nucleic Acids Res. 2017;45(D1):D1075–81.

Article 
CAS 
PubMed 

Google Scholar 

Alexandrov N, Tai SS, Wang WS, Mansueto L, Palis K, Fuentes RR, et al. SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 2015;43(D1):D1023–7.

Article 
CAS 
PubMed 

Google Scholar 

Yang WZ, Yoon J, Choi H, Fan YL, Chen RM, An G. Transcriptome analysis of nitrogen-starvation-responsive genes in rice. BMC Plant Biol. 2015;15:31.

Yan M, Fan XR, Feng HM, Miller AJ, Shen QR, Xu GH. Rice OsNAR2.1 interacts with OsNRT2.1, OsNRT2.2 and OsNRT2.3a nitrate transporters to provide uptake over high and low concentration ranges. Plant Cell Environ. 2011;34(8):1360–72.

Article 
CAS 
PubMed 

Google Scholar 

Liu XQ, Huang DM, Tao JY, Miller AJ, Fan XR, Xu GH. Identification and functional assay of the interaction motifs in the partner protein OsNAR2.1 of the two-component system for high-affinity nitrate transport. New Phytol. 2014;204(1):74–80.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Jiang HZ, Wang YM, Lai LR, Liu XT, Miao CJ, Liu RF, et al. OsAMT1.1 Expression by Nitrate-Inducible promoter of OsNAR2.1 Increases nitrogen use efficiency and rice yield. Rice Sci. 2023;30(3):222–34.

Article 

Google Scholar 

Chen HL, Xu N, Wu Q, Yu B, Chu YL, Li XX, et al. OsMADS27 regulates the root development in a NO₃-dependent manner and modulates the salt tolerance in rice (Oryza sativa L.). Plant Sci. 2018;277:20–32.

Article 
CAS 
PubMed 

Google Scholar 

Pachamuthu K, Sundar VH, Narjala A, Singh RR, Das S, Pal H, et al. Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice. J Exp Bot. 2022;73(11):3511–30.

Article 
CAS 
PubMed 

Google Scholar 

Singh RK, Khan W, editors. Effect of nitrogen levels on growth and yield of basmati rice varieties2021.

Li G, Zhang Y, Zhou C, Xu J, Cj Z, Ni C, et al. Agronomic and physiological characteristics of high yield and nitrogen use efficient varieties of rice: comparison between two near-isogenic lines. Food Energy Secur. 2024;13(2):e539.

Article 
CAS 

Google Scholar 

Tayefe M, Gerayzade A, Amiri E, Zade AN. Effect of nitrogen on rice yield, yield components and quality parameters. 2014.

Haghshenas H, Ghanbari Malidarreh A. Response of yield and yield components of released rice cultivars from 1990–2010 to nitrogen rates. Cent Asian J Plant Sci Innov. 2021;1(1):23–31.

Google Scholar 

Zhang SY, Huang YZ, Ji Z, Fang YZ, Tian YN, Shen CB, et al. Discovery of SOD5 as a novel regulator of nitrogen-use efficiency and grain yield via altering auxin level. New Phytol. 2025;246(3):1084–95.

Article 
CAS 
PubMed 

Google Scholar 

Wu J, Sun LQ, Song Y, Bai Y, Wan GY, Wang JX, et al. The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice. New Phytol. 2023;240(6):2404–18.

Article 
CAS 
PubMed 

Google Scholar 

Duan YH, Zhang YL, Ye LT, Fan XR, Xu GH, Shen QR. Responses of rice cultivars with different nitrogen use efficiency to partial nitrate nutrition. Ann Botany. 2007;99(6):1153–60.

Article 
CAS 

Google Scholar 

Tsednee M. Linking timing to nitrogen use efficiency: rice OsEC-Ghd7-ARE1 module works on it. Plant Physiol. 2024;196(3):1720–1.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Zhang L, Shen C, Zhu S, Ren N, Chen K, Xu J. Effects of sowing date and nitrogen (N) application rate on grain yield, nitrogen use efficiency and 2-acetyl-1-pyrroline formation in fragrant rice. Agronomy. 2022;12(12):3035.

Article 
CAS 

Google Scholar 

Zhang SN, Zhang YY, Li KN, Yan M, Zhang JF, Yu M, et al. Nitrogen mediates flowering time and nitrogen use efficiency via floral regulators in rice. Curr Biol. 2021;31(4):671–83.

Article 
CAS 
PubMed 

Google Scholar 

Mo Y, Jeong JM, Ha SK, Kim J, Lee C, Lee GP et al. Characterization of QTLs and candidate genes for days to heading in rice Recombinant inbred lines. Genes. 2020;11(9):957.

Song J, Tang LQ, Cui YT, Fan HH, Zhen XQ, Wang JJ. Research progress on photoperiod gene regulation of heading date in rice. Curr Issues Mol Biol. 2024;46(9):10299–311.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Reig-Valiente JL, Marqués L, Talón M, Domingo C. Genome-wide association study of agronomic traits in rice cultivated in temperate regions. BMC Genomics. 2018;19:706.

Song YL, Gao ZC, Luan WJ. Interaction between temperature and photoperiod in regulation of flowering time in rice. Sci China-Life Sci. 2012;55(3):241–9.

Article 
CAS 
PubMed 

Google Scholar 

Matsubara K, Yamanouchi U, Wang ZX, Minobe Y, Izawa T, Yano M. Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating Ehd1. Plant Physiol. 2008;148(3):1425–35.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 

Ohkubo Y, Kuwata K, Matsubayashi Y. A type 2 C protein phosphatase activates high-affinity nitrate uptake by dephosphorylating NRT2.1. Nat Plants. 2021;7(3):310.

Article 
CAS 
PubMed 

Google Scholar 

Wu JY, Yang SQ, Chen NA, Jiang QN, Huang LL, Qi JX et al. Nuclear translocation of OsMADS25 facilitated by OsNAR2.1 in reponse to nitrate signals promotes rice root growth by targeting OsMADS27 and OsARF7. Plant Commun. 2023;4(6):100642.

Alfatih A, Zhang J, Song Y, Jan SU, Zhang ZS, Xia JQ et al. Nitrate-responsive OsMADS27 promotes salt tolerance in rice. Plant Commun. 2023;4(2):100458.

Song X, Xiong Y, Kong X, Huang G. Roles of auxin response factors in rice development and stress responses. Plant Cell Environ. 2023;46(4):1075–86.

Article 
CAS 
PubMed 

Google Scholar 

Zhang S, Wu T, Liu S, Liu X, Jiang L, Wan J. Disruption of OsARF19 is critical for floral organ development and plant architecture in rice (Oryza sativa L). Plant Mol Biology Report. 2016;34:748–60.

Article 
CAS 

Google Scholar 

Gho YS, Song MY, Bae DY, Choi H, Jung KH. Rice PIN auxin efflux carriers modulate the nitrogen response in a changing nitrogen growth environment. Int J Mol Sci. 2021;22(6):3243.

Zhang S, Zhu L, Shen C, Ji Z, Zhang H, Zhang T, et al. Natural allelic variation in a modulator of auxin homeostasis improves grain yield and nitrogen use efficiency in rice. Plant Cell. 2020;33(3):566–80.

Article 
PubMed Central 

Google Scholar 

Zhang S, Wang S, Xu Y, Yu C, Shen C, Qian Q, et al. The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3-5 and OsBRI1. Plant Cell Environ. 2015;38(4):638–54.

Article 
PubMed 

Google Scholar 

Wu D, Cao Y, Wang D, Zong G, Han K, Zhang W, et al. Auxin receptor OsTIR1 mediates auxin signaling during seed filling in rice. Plant Physiol. 2024;194(4):2434–48.

Article 
CAS 
PubMed 

Google Scholar 

Cortes LT, Zhang ZW, Yu JM. Status and prospects of genome-wide association studies in plants. Plant Genome. 2021;14(1):e20077.

Curtin SJ, Tiffin P, Guhlin J, Trujillo DI, Burghardt LT, Atkins P, et al. Validating genome-wide association candidates controlling quantitative variation in nodulation. Plant Physiol. 2017;173(2):921–31.

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar